How To Find Methylated And Un-Methylated Regions(Cpg Islands) In Given Wgs Of Different Species

Question

[Repineme]

I checked "epigraph" and "hdmfinder". These tools are not universal, means if I use different organs of different species they may fail. Is there anyway I can find both methylated and un-methylated regions in DNA (WGS). Is it easy to write a script ?

Thanx

Answer 1

[Chris Miller]

Normal DNA sequencing does not give you information about the methylation status of DNA. For that you'll have to use a method like bisulfite sequencing or an immunoprecipitation method like MeDIP-seq.

If you're just looking for CpG islands, I recommend downloading the CpGIslands track from UCSC:

[Larry_Parnell]

Furthermore, methylation status is both time- and tissue-dependent. The source of the DNA used in a WGS analysis is not always made available, or is a mixture. Thus, any methylation signals obtained, by the appropriate methods, like MeDIP-seq, would be suspect. A fresh tissue sample as pure as possible is necessary.